Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   
6  
 5'  3'   
7  
 5'  3'   
8  
 5'  3'   
9  
 5'  3'   
10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA

Basic information

species Oryza sativa
transcript LOC_Os05g06430.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G404011_T01 (Zea mays), 3'ss of exon 4
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA
|||||||| | || ||| ||| || |||| || |||| | | || | |||| | | ||| ||| || ||||| ||||||||||||||||||| ||||| |||| || || || || |||||||| ||||||||||||||||||||||| ||||||| |||||| || ||
gttagtagagtat-----tagcttgaaaatttccaaattattgcagcg--gtcttcattttttttgtggact-gaacatgtacttgaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAACAGGACGACGGTGTTGTGATTGCCAATCTTGATGCTGACAAGCACACTGACTTGGCTGAAAA

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G170845_T01 (Zea mays), 3'ss of exon 2
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA
|||||||| | || ||| ||| || |||| || |||| | | ||| |||| | | ||| ||| || ||||| ||||||||||||||||||| ||||| |||| ||||| || || ||| |||| ||||||||||||||||||||||| ||||||| |||||| || ||
gttagtagagtat-----tagcttgaaaatttccaaattattgcagcg---gtcttcatttttttgtggact-gaacatgtacttgaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTATTGTGATTGCCAATCTTGATGCTGACAAGCACACTGACTTGGCTGAAAA

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G159369_T02 (Zea mays), 3'ss of exon 6
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA--------
|||||||| | || ||| ||| || |||| || |||| | | || | |||| | | ||| ||| || |||| ||||||||||||||||||| ||||| |||| ||||| || || |||||||| ||||||||| ||||||||||||| ||||||| |||||| || ||
gttagtagagtat-----tagcttgaaaatttccaaattattgcagcg--gtcttcattttttttgtggact-gaacatgtacttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAAGTATGCAT

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AC199571.3_FGT004 (Zea mays), 3'ss of exon 3
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA--------
|||||||| | || ||| ||| || |||| || |||| | | || | |||| | | ||| ||| || ||||| ||||||||||||||||||| ||||| |||| ||||| || || ||||||| ||||||||||||||||||||||| ||||||| ||||| || ||
gttagtagagtat-----tagcttgaaaatttccaaattattgcagcg--gtcttcattttttttgtggact-gaacatgtacttgaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACAGTGTTGTGATTGCCAATCTTGATGCTGACAAGCACACTGACTTGGATGAAAAGTATGCAT

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 6
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA
|||||||| | || ||| ||| || |||| || |||| | | || | |||| | | ||| ||| || |||| ||||||||||||||||||| ||||| |||| ||||| || || |||||||| ||||||||| ||||||||||||| ||||||| |||||| || ||
gttagtagagtat-----tagcttgaaaatttccaaattattgcagcg--gtcttcattttttttgtggact-gaacatgtacttaaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACGGTGTTGTGATTGCCAATATTGATGCTGACAAGCACACTGACTTGGCTGAAAA

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 3
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgt-tttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA
|||||||| | || ||| ||| || |||| || |||| | | || | |||| | | ||| ||| || ||||| ||||||||||||||||||| ||||| |||| ||||| || || ||||||| ||||||||||||||||||||||| ||||||| |||||| | ||
gttagtagagtat-----tagcttgaaaatttccaaattattgcagcg--gtcttcattttttttgtggact-gaacatgtacttgaatttagATTTATGAGAAGCTGGCTTCAGTTTTCAAGCAGGACGACAGTGTTGTGATTGCCAATCTTGATGCTGACAAGCACACTGACTTGGCTAAAAA

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G110742_T02 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------gttagtagta-cacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA
||||| || | | || ||| ||| || |||| || |||| | || ||||||| | ||| ||| || ||||| |||||||||||||| ||||| |||| ||||| || | ||||||| ||||||||||||||||||||||| ||||||| |||||| || ||
gtgcttatgaaagtttttacctattcttcaatatgaagtctgaatgtgtggtgtggcctgtctgatctatctagcaggtttagtgttagtagagtattagcttgaaaatttccaaattattgcagcggt-cttcattattttg--tggact-gaacatgtacttg-----aatttatgagaagCTGGCTTCAGTTTTCAAGCAGGACAACAGTGTTGTGATTGCCAATCTTGATGCTGACAAGCACACTGACTTGGCTGAAAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58662435|gb|CK051121.1|CK051121
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCT
EST: gi|58684543|gb|CK073230.1|CK073230
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGG
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGG
EST: gi|27577315|gb|CB000010.1|CB000010
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|58653948|gb|CK042628.1|CK042628
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTGAGTGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTAT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTA-TGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTAT
EST: gi|58659841|gb|CK048521.1|CK048521
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|58690891|gb|CK079578.1|CK079578
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|12622813|gb|AU173026.1|AU173026
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     GTGTGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
EST: gi|58675064|gb|CK063751.1|CK063751
EST:     GTGCGGTCACTGCAAGCATCTTGCTCCG                         ATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT
genomic: GTGTGGTCACTGCAAGCATCTTGCTCCGgttagtagta ... cttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA
                          gtctaaa  putative branch site (score: 3)
 cttgtttt  putative PPT
 tcatttttctatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtagtacacctcagtattttgcaaagttgcaaaataatgcattgtcatttttctattttgtctaaactcaaacttgcacttgttttagATTTATGAGAAGCTAGCTTCTGTTTATAAGCAAGATGAGGGTGTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG